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Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2

Analyse Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8I9Y
Type: protein + RNA
Length: 14,914 residues
Chains: 59
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.1
Source: Chaetomium thermophilum
Molecule: RNA (3341-mer); RNA (319-mer); Brix domain-containing protein; Ribosome biogenesis…
EC: 2.4.99.18
UniProt: G0RXZ3, G0S7X0, G0SCK6, G0SFB5, G0RYU9, G0S616, G0S435, G0S8F1, G0S1H0, G0SHX6, G0S081, G0SEW3, G0SFL0, G0S683, G0SHK0, G0SHQ0, G0S497, G0S832, G0SGD8, G0S5L0, G0SGC2, G0SHJ6, G0SGJ0, G0SD05, G0SCP3, G0RXW1, G0SFC3, G0S0D6, G0SAJ9, G0S0E5, G0SGH8, G0S992, G0S1R0, G0RZ88, G0SH61, G0SGY1, G0S9B5, G0S9T3, G0SCE2, G0S0Z3, G0SDS8, G0SI44, G0S507, G0RYN9, G0RZE9, G0SEI0, G0SD68, G0S6V4, G0SCL3, G0SFN0, G0S0D7, G0SBN1, G0S101, G0SG89, Q2H9R2, G0S4Z9
Ligands: GTP, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 3.1 · 59 distinct chains · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C1	RNA (3341-mer)	rna	2609	—	—
C2	RNA (319-mer)	rna	256	—	—
CA	Brix domain-containing protein	protein	251	28% helix, 32% strand	G0RXZ3
CB	Ribosome biogenesis protein C8F11.04	protein	260	38% helix, 20% strand	G0S7X0
CC	Ribosome biogenesis protein ERB1	protein	658	15% helix, 29% strand	G0SCK6
CD	Ribosome biogenesis protein YTM1	protein	460	8% helix, 44% strand	G0SFB5
CE	RNA helicase	protein	462	44% helix, 14% strand	G0RYU9
CF	Ribosome assembly factor mrt4	protein	245	29% helix, 20% strand	G0S616
CG	60S ribosome subunit biogenesis protein NIP7	protein	177	29% helix, 33% strand	G0S435
CH	Nucleolar GTP-binding protein 1	protein	542	51% helix, 8% strand	G0S8F1
CI	Putative RNA-binding protein	protein	146	33% helix, 21% strand	G0S1H0
CJ	Pescadillo homolog	protein	494	54% helix, 9% strand	G0SHX6
CK	Ribosome biogenesis protein NSA2 homolog	protein	229	41% helix, 18% strand	G0S081
CL	Putative GTP binding protein	protein	397	41% helix, 8% strand	G0SEW3
CM	60S ribosomal protein l7-like protein	protein	223	50% helix, 15% strand	G0SFL0
CN	Eukaryotic translation initiation factor 6	protein	246	33% helix, 26% strand	G0S683
CO	DUF2423 domain-containing protein	protein	62	63% helix, 0% strand	G0SHK0
CP	RNA methyltransferase nop2-like protein	protein	356	40% helix, 18% strand	G0SHQ0
CQ	Ribosome biogenesis protein RLP24	protein	179	51% helix, 8% strand	G0S497
CR	Nucleolar protein 16	protein	167	40% helix, 2% strand	G0S832
CS	AdoMet-dependent rRNA methyltransferase SPB1	protein	262	49% helix, 6% strand	G0SGD8
CT	Nucleolar complex-associated protein 3	protein	488	70% helix, 0% strand	G0S5L0
CU	rRNA-processing protein EBP2	protein	178	65% helix, 3% strand	G0SGC2
CV	Putative 60S ribosomal protein	protein	139	33% helix, 17% strand	G0SHJ6
CX	60S ribosomal subunit-like protein	protein	88	53% helix, 2% strand	G0SGJ0
CY	Putative NOC2 family protein	protein	420	70% helix, 1% strand	G0SD05
Cz	rRNA-processing protein	protein	70	63% helix, 0% strand	G0SCP3
LB	60S ribosomal protein L3-like protein	protein	356	19% helix, 32% strand	G0RXW1
LC	60S ribosomal protein L4-like protein	protein	362	37% helix, 10% strand	G0SFC3
LE	60S ribosomal protein L6	protein	179	28% helix, 17% strand	G0S0D6
LF	60S ribosomal protein l7-like protein	protein	247	55% helix, 14% strand	G0SFL0
LG	60S ribosomal protein L8	protein	204	56% helix, 8% strand	G0SAJ9
LH	60S ribosomal protein l9-like protein	protein	190	22% helix, 41% strand	G0S0E5
LK	60S ribosomal protein L12-like protein	protein	146	42% helix, 11% strand	G0SGH8
LL	60S ribosomal protein L13	protein	117	42% helix, 15% strand	G0S992
LM	60S ribosomal protein L14-like protein	protein	137	43% helix, 28% strand	G0S1R0
LN	Ribosomal protein L15	protein	183	42% helix, 16% strand	G0RZ88
LO	60S ribosomal protein L16-like protein	protein	204	56% helix, 12% strand	G0SH61
LP	60S ribosomal protein l17-like protein	protein	169	38% helix, 25% strand	G0SGY1
LQ	Ribosomal protein L18-like protein	protein	129	40% helix, 19% strand	G0S9B5
LR	Ribosomal protein L19	protein	119	64% helix, 5% strand	G0S9T3
LS	60S ribosomal protein L20	protein	174	23% helix, 33% strand	G0SCE2
LT	60S ribosomal protein l21-like protein	protein	126	20% helix, 29% strand	G0S0Z3
LU	60S ribosomal protein L22-like protein	protein	105	30% helix, 31% strand	G0SDS8
LV	60S ribosomal protein l23-like protein	protein	135	8% helix, 37% strand	G0SI44
LX	60S ribosomal protein L25-like protein	protein	137	36% helix, 18% strand	G0S507
LY	60S ribosomal protein L26-like protein	protein	134	34% helix, 27% strand	G0RYN9
LZ	60S ribosomal protein L27	protein	135	33% helix, 24% strand	G0RZE9
Lc	60S ribosomal protein l30-like protein	protein	98	46% helix, 17% strand	G0SEI0
Ld	Putative 60S ribosomal protein	protein	109	28% helix, 29% strand	G0SD68
Le	60S ribosomal protein L32-like protein	protein	127	24% helix, 9% strand	G0S6V4
Lf	60S ribosomal protein l33-like protein	protein	108	6% helix, 48% strand	G0SCL3
Lg	Ribosomal protein l34-like protein	protein	117	41% helix, 12% strand	G0SFN0
Lh	dolichyl-diphosphooligosaccharide--protein glycotransferase (EC 2.4.99.18)	protein	121	64% helix, 3% strand	G0S0D7
Li	60S ribosomal protein L36	protein	88	70% helix, 1% strand	G0SBN1
Lj	Ribosomal protein L37	protein	74	18% helix, 8% strand	G0S101
Lk	60S ribosomal protein L38-like protein	protein	75	25% helix, 33% strand	G0SG89
Ll	60S ribosomal protein L39	protein	38	47% helix, 0% strand	Q2H9R2
Lq	Ribosomal protein	protein	207	38% helix, 14% strand	G0S4Z9

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains CH
ZN · Zinc ion · metal · 2 copies · chains CQ, Lj

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	924	0.89	0.92	89	empty
2	1045	0.88	0.90	109	empty
3	774	0.88	0.92	80	empty
4	692	0.88	0.93	77	empty
5	1124	0.87	0.88	108	empty

Interfaces

228 interfaces between chains.

C1–LC · 8211 Å² buried · 161 hydrogen bonds · protein-nucleic
C1–LB · 6597 Å² buried · 150 hydrogen bonds · protein-nucleic
C1–LN · 5646 Å² buried · 113 hydrogen bonds · protein-nucleic
C1–C2 · 4964 Å² buried · 275 hydrogen bonds · nucleic-nucleic
C1–LO · 4691 Å² buried · 80 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

G0SFB5 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein YTM1 (G0SFB5) · a predicted model of the same protein · chain CD against A, TM-score 0.91
G0S8F1 · AlphaFold monomer V2.0 prediction for nucleolar GTP-binding protein 1 (G0S8F1) · a predicted model of the same protein · chain CH against A, TM-score 0.88
G0S616 · AlphaFold monomer V2.0 prediction for ribosome assembly factor MRT4 (G0S616) · a predicted model of the same protein · chain CF against A, TM-score 0.76
G0SCK6 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein ERB1 (G0SCK6) · a predicted model of the same protein · chain CC against A, TM-score 0.72

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